| Supervised machine learning outperforms taxonomy‐based environmental DNA metabarcoding applied to biomonitoring T Cordier, D Forster, Y Dufresne, CIM Martins, T Stoeck, J Pawlowski Molecular ecology resources 18 (6), 1381-1391, 2018 | 155 | 2018 |
| Norine: Update of the nonribosomal peptide resource A Flissi, E Ricart, C Campart, M Chevalier, Y Dufresne, J Michalik, ... Nucleic acids research 48 (D1), D465-D469, 2020 | 104 | 2020 |
| SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data Y Dufresne, F Lejzerowicz, LA Perret-Gentil, J Pawlowski, T Cordier BMC bioinformatics 20, 1-6, 2019 | 78 | 2019 |
| Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing A Flissi, Y Dufresne, J Michalik, L Tonon, S Janot, L Noé, P Jacques, ... Nucleic acids research 44 (D1), D1113-D1118, 2016 | 62 | 2016 |
| MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes P Pericard, Y Dufresne, L Couderc, S Blanquart, H Touzet Bioinformatics 34 (4), 585-591, 2018 | 53 | 2018 |
| Norine: A powerful resource for novel nonribosomal peptide discovery M Pupin, Q Esmaeel, A Flissi, Y Dufresne, P Jacques, V Leclère Synthetic and systems biotechnology 1 (2), 89-94, 2016 | 36 | 2016 |
| Comparing methods for constructing and representing human pangenome graphs F Andreace, P Lechat, Y Dufresne, R Chikhi Genome biology 24 (1), 274, 2023 | 24 | 2023 |
| Smiles2Monomers: a link between chemical and biological structures for polymers Y Dufresne, L Noé, V Leclère, M Pupin Journal of cheminformatics 7, 1-11, 2015 | 20 | 2015 |
| The K-mer File Format: a standardized and compact disk representation of sets of k-mers Y Dufresne, T Lemane, P Marijon, P Peterlongo, A Rahman, M Kokot, ... Bioinformatics 38 (18), 4423-4425, 2022 | 13 | 2022 |
| Compression algorithm for colored de Bruijn graphs A Rahman, Y Dufresne, P Medvedev Algorithms for Molecular Biology 19 (1), 20, 2024 | 5 | 2024 |
| Construction and representation of human pangenome graphs F Andreace, P Lechat, Y Dufresne, R Chikhi bioRxiv, 2023.06. 02.542089, 2023 | 3 | 2023 |
| A Graph-Theoretic Barcode Ordering Model for Linked-Reads Y Dufresne, C Sun, P Marijon, D Lavenier, C Chauve, R Chikhi WABI 2020-20th Workshop on Algorithms in Bioinformatics, 11-12, 2020 | 2 | 2020 |
| The Backpack Quotient Filter: a dynamic and space-efficient data structure for querying k-mers with abundance. V Levallois, F Andreace, B Le Gal, Y Dufresne, P Peterlongo bioRxiv, 2024.02. 15.580441, 2024 | 1 | 2024 |
| BioConvert: a comprehensive format converter for life sciences H Caro, S Dollin, A Biton, B Brancotte, D Desvillechabrol, Y Dufresne, B Li, ... NAR Genomics and Bioinformatics 5 (3), lqad074, 2023 | 1 | 2023 |
| Reconstruction of full-length 16S rRNA sequences for taxonomic assignment in metagenomics P Pericard, Y Dufresne, S Blanquart, H Touzet JOBIM 2017-Journées Ouvertes en Biologie, Informatique et Mathématiques, 2017 | 1 | 2017 |
| Constructing and personalizing population pangenome graphs R Chikhi, Y Dufresne, P Medvedev Nature Methods, 1-2, 2024 | | 2024 |
| Efficient dynamic associative dictionary for large k-mer sets Y Dufresne, C Marchet, R Chikhi, A Limasset BMC BIOINFORMATICS 21 (SUPPL 20), 2020 | | 2020 |
| Read correction for non-uniform coverages C Marchet, Y Dufresne, A Limasset bioRxiv, 673624, 2019 | | 2019 |
| MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes Y Dufresne, L Couderc, S Blanquart, H Touzet Oxford University Press (OUP), 2017 | | 2017 |
| Norine, Florine, s2m: powerful bioinformatics resource and tools for the discovery of novel nonribosomal peptides, natural metabolites with versatile activities Q Esmaeel, Y Dufresne, A Flissi, M Pupin, P Jacques, V Leclère FEMS 2017-7th congress of Federation of European Microbiology societies, 2017 | | 2017 |
Maude PupinMaître de conférences en informatique, Université de LilleEmail verificata su univ-lille.fr